I love your ideas, especially when it comes to Count Doku. I always thought he should have been in the first movie. (along with a few other characters, I had posted some great ideas in the “radical prequel ideas” thread I think.) I have a suggestion though. Could you somehow remove Jar Jar from Tattoine entirely? (lets say that he never left the ship as since he is useless he has no purpose fallowing them along.) And remove little Anakin from the final battle? (lets say that he stayed at the Jedi Temple. Because why would they bring a child along to the war zone?)
That would make the movie much much better I think. (I tried to do just that in my edit but I no longer have the time)
I’m sure a decent cut could be made without Jar Jar on Tatooine and Anakin absent from the climax, but that’s not currently what my goals are. I’ve rewritten Jar Jar to have much more of a purpose, and he really needs to be on Tatooine for at least a few scenes in particular.
And In my edit, Anakin destroying the control ship is what wins the whole battle for everyone. He also has a big “use the force” moment in the climax that I think really helps his character arc.
So, yea. Those scenes will remain, at least in my edit. But I’m sure there are cuts out there that do what you’re suggesting.